Genome-wide maps of RNA-protein interactions of SRSF3, hnRNPK and CPSF6

C2C12 cells were UV-irradiated at 400 mJ, and whole cell lysates were harvested from the cells. tRIP was performed as previously described (Masuda et al). Samples were sequenced on the Illumina NovaSeq6000 with 150 bp paired-end read (Macrogen, Japan) or Miseq with 150 bp single-read at the core facility of the Nagoya University. For paired-end read data, only P5 reads were used for analysis. Briefly, after standard HiSeq demultiplexing, reads were adapter-trimmed and reads less than 18 bp were discarded using cutadapt (v1.10). Mapping was first performed against the mouse repetitive elements in RepBase with STAR (v2.5.2b). Repeat-mapped reads were removed, and all others were then mapped against the mouse genome (mm10) with STAR (v 2.5.2b). Multiply mapped reads were filtered out. Duplicates of reads uniquely mapped to the human or mouse genome were removed by Picard (v2.0.1). Genome-wide maps of binding sites of RNA-binding proteins